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| 1 | Design of 16S rRNA gene primers for 454 pyrosequencing of the human foregut microbiome显示文摘AIM:To design and validate broad-range 16S rRNA primers for use in high throughput sequencing to classify bacteria isolated from the human foregut microbiome.METHODS:A foregut microbiome dataset was constructed using 16S rRNA gene sequences obtained from oral,esophageal,and gastric microbiomes produced by Sanger sequencing in previous studies represented by 219 bacterial species.Candidate primers evaluated were from the European rRNA database.To assess the effect of sequence length on accuracy of classification,16S rRNA genes of various lengths were created by trimming the full length sequences.Sequences spanning various hypervariable regions were selected to simulate the amplicons that would be obtained using possible primer pairs.The sequences were compared with full length 16S rRNA genes for accuracy in taxonomic classification using online software at the Ribosomal Database Project (RDP).The universality of the primer set was evaluated using the RDP 16S rRNA database which is comprised of 433 306 16S rRNA genes,represented by 36 phyla.RESULTS:Truncation to 100 nucleotides(nt)downstream from the position corresponding to base 28 in the Escherichia coli 16S rRNA gene caused misclassification of 87(39.7%)of the 219 sequences,compared with misclassification of only 29(13.2%)sequences with truncation to 350 nt.Among 350-nt sequence reads within various regions of the 16S rRNA gene,the reverse read of an amplicon generated using the 343F/798R primers had the least(8.2%)effect on classification.In comparison,truncation to 900 nt mimicking single pass Sanger reads misclassified 5.0%of the 219 sequences.The 343F/798R amplicon accurately assigned 91.8%of the 219 sequences at the species level.Weighted by abundance of the species in the esophageal dataset,the 343F/798R amplicon yielded similar classification accuracy without a significant loss in species coverage(92%).Modification of the 343F/798R primers to 347F/803R increased their universality among foregut species.Assuming that a typicalpolymerase chain reaction can tolerate 2 mismatches between a primer and a template,the modified 347F and 803R primers should be able to anneal 98%and 99.6%of all 16S rRNA genes in the RDP database.CONCLUSION:347F/803R is the most suitable pair of primers for classification of foregut 16S rRNA genes but also possess universality suitable for analyses of other complex microbiomes. | Carlos W Nossa William E Oberdorf Jφrn A Aas Bruce J Paster Todd Z DeSantis Eoin L Brodie Daniel Malamud Michael A Poles Zhiheng Pei | 2010 | World Journal of Gastroenterology2010，16，33： | 16 |
| 2 | Thomashow components of the Arabidopsis C repeat/dehydration responsive element bindingfactor cold-response pathway are conserved in Brassica napus and other plant species显示文摘 | KIRSTEN R J SUSANNE K KEENAN L A XIN Z VOLKER H JAMES Z Z THOMAS D MICHAEL F | 2001 | Plant Plzysiology2001，127，3： | 1 |
| 3 | Effects of interactive scale-dependent variables on beetle diversity patterns in a semi-arid agricultural landscape 显示文摘 | Gal Y Yaron Z Michael L R | 2007 | Landscape Ecology2007，，22： | 1 |
| 4 | Restoration of insulin-sensitive glucose transporter(GLUT4) gene expression in muscle cells by the transcriptional coactivator PGC-1显示文摘 | Michael L F Wu Z Cheatham R B | 2001 | Proc Natl Acad Sci U S A2001，98，： | 1 |
| 5 | Restoration of insulin-sensitive glucose transporter (GLUT4) gene expres- sion inmusele cells by the transcriptional coactivator PGC-1 显示文摘 | Michael L F Wu Z Cheatham R B | 2001 | Proc Natl Acad Sci USA2001，98，： | 1 |
| 6 | Restoration of insulin-sensitive glucose transporter (GLUT4) gene expres- sion in muscle cells by the transcriptional coactivator PGC-1 显示文摘 | Michael L F Wu Z Cheatham R B | 2001 | Proc Natl Acad Sci U S A2001，98，7： | 1 |
| 7 | Restoration of insulin-sensitive glucose transporter (GLUT4) gene expression in muscle cells by the transcriptional coactivator PGC-1显示文摘 | Michael L F Wu Z Cheatham R B | 2001 | Proc Natl Acad Sci USA2001，98，： | 1 |
| 8 | Control of pollen tube tip growth by a Rop GTPase dependent pathway that leads to tip localized calcium influx显示文摘 | Hal L Yakang L Rachel H Michael Z | 1999 | Plant Cell1999，11，： | 1 |
| 9 | Current methods for loading dendritic cells with tumor antigen for the induction of antitumor immunity显示文摘 | Bosch Z Marnix L Michael L | 2002 | Immunotherapy2002，25，： | 1 |
| 10 | Leukocyte trafficking and myocardial reperfusion injury in ICAM-1/P-selectin-knockout mice显示文摘 | Briaud S A Ding Z M Michael L H | 2001 | Am J physiol Heart Circ Physiol2001，280，1： | 1 |
| 11 | A view of cloud computing显示文摘 | MICHAEL A ARMANDO F REAN Q ANTHONY D J RANDY K ANDY K GUNHO L DAVID P ARIEL R ION S MATEI Z | 2010 | Communications of the ACM2010，53，4： | 1 |
| 12 | Peptides from frog skin 显示文摘 | Charles L B Michael Z | 1990 | Annu RevBiochem1990，59，： | 1 |
| 13 | Predicting ripple roughness and sand resuspension under combined flows in a shoreface environment显示文摘 | Michael Z L Wright L D Carl L A | 1996 | Marine Geology1996，130，12： | 1 |
| 14 | Adaptive traffic signal control with vehicular ad hoc networks显示文摘 | KARTIK P DIPAK G L MICHAEL H Z | 2013 | IEEE Transaotions on Ve- hicular Technology2013，62，4： | 1 |
| 15 | Multibeam bathymetric in vestigations of the morphology of sand ridges and associated hedforms and their relation to storm process, Sable Island Bank, Scotian Shelf 显示文摘 | Michael Z Li Edward L King | 2007 | Marine Geology2007，243，14： | 1 |
| 16 | Sparse linear discriminant analysis for simultaneous testing for the significance of a gene set/pathway and gene selection 显示文摘 | Michael C Wu Zhang L S Wang Z X | 2009 | Original Paper2009，25，9： | 1 |
| 17 | CD80 and CD86 differentially modulate the suppressive function of human regulatory T cells 显示文摘 | Yong Z Claire N M Michael L | 2004 | J Immunol2004，172，5： | 1 |
| 18 | Upgrade to iterative image reconstruction (IR) in MDCT imaging: a clinical study for detailed parameter optimization beyond vendor recommendations using the adaptive statistical iterative reconstruction environment (ASIR) Part2: The chest显示文摘 | Mucck FG Michael L Deak Z | 2013 | Role2013，185，7： | 1 |
| 19 | Use of a new thrombus extraction catheter(The ProntoR) in the treatment of acute myocardial infarction显示文摘 | Michael J L Lisa R Ali Z | 2005 | J of Interventional Cardiol2005，18，： | 1 |
| 20 | How to Build Trust On-line显示文摘 | Dayal S Helene L Michael Z | 2010 | Marketing Management2010，44，3： | 1 |
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